X-PLOR: V3.834 user: on: Alpha/OSF at: 27-Apr-96 13:40:38 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! make-template.inp -- Build extended structure for local geometry reference X-PLOR>! Dave Schweisguth , 27 Apr 1996 X-PLOR>! Derived from nmr/generate_template.inp X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use xplor -s ASSFIL: file /sgi/people/dcs/ws/xplor/italy2.4x/xplor.seed opened. SEED=58618.5152893066 SET> end ! Use xplor -s X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) X-PLOR> X-PLOR>vector ident (x) (all) ! Set X coordinate to atom number(!) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (x=x/10) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (y=random(0.5)) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (z=random(0.5)) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (fbeta=50) (all) ! Friction coefficient, in 1/ps SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (mass=100) (all) ! Heavy masses, in amu SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> cutnb=5.5 NBDSET> rconst=20 NBDSET> nbxmod=-2 NBDSET> repel=0.9 ! Repulsive non-bonded energy only NBDSET> wmin=0.1 NBDSET> tolerance=1 NBDSET> rexp=2 ! default NBDSET> irexp=2 ! default NBDSET> inhibit=0.25 NBDSET> end PARRDR>end X-PLOR> X-PLOR>! Parameter set may or may not contain dihedral energies X-PLOR> X-PLOR>flags exclude * include bond angle dihe vdw end X-PLOR>minimize powell nstep=200 nprint=10 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 34342 intra-atom interactions %atoms "A -13 -ADE -H3' " and "A -14 -ADE -O5' " only 0.08 A apart NBONDS: found 33081 intra-atom interactions %atoms "A -5 -GUA -H8 " and "A -5 -GUA -O2' " only 0.08 A apart %atoms "A -13 -ADE -H3' " and "A -14 -ADE -O5' " only 0.09 A apart NBONDS: found 32305 intra-atom interactions %atoms "A -5 -GUA -O1P " and "A -5 -GUA -O5' " only 0.04 A apart NBONDS: found 28538 intra-atom interactions NBONDS: found 30324 intra-atom interactions NBONDS: found 30262 intra-atom interactions %atoms "A -17 -CYT -H42 " and "A -17 -CYT -C2' " only 0.08 A apart NBONDS: found 29955 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =0.47E+07 grad(E)=2668.897 E(BOND)=0.11E+07 E(ANGL)=641744.764 | | E(DIHE)=0.000 E(VDW )=0.29E+07 | ------------------------------------------------------------------------------- NBONDS: found 28641 intra-atom interactions NBONDS: found 24657 intra-atom interactions NBONDS: found 24440 intra-atom interactions NBONDS: found 21863 intra-atom interactions NBONDS: found 20901 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0000 ----------------------- | Etotal =0.19E+07 grad(E)=1671.958 E(BOND)=675037.685 E(ANGL)=289153.315 | | E(DIHE)=0.000 E(VDW )=945336.581 | ------------------------------------------------------------------------------- NBONDS: found 19561 intra-atom interactions NBONDS: found 18979 intra-atom interactions NBONDS: found 18294 intra-atom interactions NBONDS: found 17395 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0000 ----------------------- | Etotal =965669.628 grad(E)=947.115 E(BOND)=299576.230 E(ANGL)=172779.146 | | E(DIHE)=0.000 E(VDW )=493314.253 | ------------------------------------------------------------------------------- NBONDS: found 16641 intra-atom interactions NBONDS: found 16060 intra-atom interactions NBONDS: found 15620 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0000 ----------------------- | Etotal =629438.289 grad(E)=640.764 E(BOND)=202330.574 E(ANGL)=108425.859 | | E(DIHE)=0.000 E(VDW )=318681.856 | ------------------------------------------------------------------------------- NBONDS: found 15027 intra-atom interactions NBONDS: found 14505 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =452437.576 grad(E)=451.348 E(BOND)=151201.807 E(ANGL)=77747.752 | | E(DIHE)=0.000 E(VDW )=223488.017 | ------------------------------------------------------------------------------- NBONDS: found 13988 intra-atom interactions NBONDS: found 13510 intra-atom interactions NBONDS: found 13180 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =355968.366 grad(E)=357.145 E(BOND)=134422.161 E(ANGL)=61487.933 | | E(DIHE)=0.000 E(VDW )=160058.272 | ------------------------------------------------------------------------------- NBONDS: found 12875 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =302079.522 grad(E)=257.752 E(BOND)=116632.474 E(ANGL)=46947.600 | | E(DIHE)=0.000 E(VDW )=138499.447 | ------------------------------------------------------------------------------- NBONDS: found 12698 intra-atom interactions NBONDS: found 12407 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =266504.613 grad(E)=235.279 E(BOND)=105656.121 E(ANGL)=39842.133 | | E(DIHE)=0.000 E(VDW )=121006.360 | ------------------------------------------------------------------------------- NBONDS: found 12210 intra-atom interactions NBONDS: found 11970 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =239551.034 grad(E)=192.858 E(BOND)=99357.903 E(ANGL)=33864.154 | | E(DIHE)=0.000 E(VDW )=106328.977 | ------------------------------------------------------------------------------- NBONDS: found 11694 intra-atom interactions NBONDS: found 11558 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =221350.534 grad(E)=158.292 E(BOND)=92792.092 E(ANGL)=27994.976 | | E(DIHE)=0.000 E(VDW )=100563.466 | ------------------------------------------------------------------------------- NBONDS: found 11341 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =209025.257 grad(E)=146.248 E(BOND)=94705.064 E(ANGL)=22841.455 | | E(DIHE)=0.000 E(VDW )=91478.738 | ------------------------------------------------------------------------------- NBONDS: found 11026 intra-atom interactions NBONDS: found 10851 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =196796.558 grad(E)=128.472 E(BOND)=88521.484 E(ANGL)=19428.564 | | E(DIHE)=0.000 E(VDW )=88846.510 | ------------------------------------------------------------------------------- NBONDS: found 10689 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =187599.214 grad(E)=116.452 E(BOND)=88778.460 E(ANGL)=16367.340 | | E(DIHE)=0.000 E(VDW )=82453.415 | ------------------------------------------------------------------------------- NBONDS: found 10448 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =181095.734 grad(E)=101.495 E(BOND)=85774.147 E(ANGL)=14131.545 | | E(DIHE)=0.000 E(VDW )=81190.042 | ------------------------------------------------------------------------------- NBONDS: found 10319 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =175556.629 grad(E)=83.070 E(BOND)=86147.124 E(ANGL)=12206.879 | | E(DIHE)=0.000 E(VDW )=77202.625 | ------------------------------------------------------------------------------- NBONDS: found 10153 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =171326.230 grad(E)=74.260 E(BOND)=84978.872 E(ANGL)=10653.186 | | E(DIHE)=0.000 E(VDW )=75694.172 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =168418.243 grad(E)=69.578 E(BOND)=84265.766 E(ANGL)=9806.742 | | E(DIHE)=0.000 E(VDW )=74345.735 | ------------------------------------------------------------------------------- NBONDS: found 9998 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0000 ----------------------- | Etotal =165981.647 grad(E)=56.797 E(BOND)=84342.315 E(ANGL)=9065.158 | | E(DIHE)=0.000 E(VDW )=72574.174 | ------------------------------------------------------------------------------- NBONDS: found 9842 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0000 ----------------------- | Etotal =164239.057 grad(E)=50.714 E(BOND)=83241.052 E(ANGL)=8353.091 | | E(DIHE)=0.000 E(VDW )=72644.914 | ------------------------------------------------------------------------------- NBONDS: found 9737 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =163039.560 grad(E)=40.262 E(BOND)=83067.218 E(ANGL)=8027.299 | | E(DIHE)=0.000 E(VDW )=71945.043 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>flags include impr end X-PLOR>minimize powell nstep=200 nprint=10 end POWELL: number of degrees of freedom= 2031 CODIMP: improper type-based parameters retrieved NBONDS: found 9718 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =404631.149 grad(E)=288.211 E(BOND)=86392.279 E(ANGL)=39036.915 | | E(DIHE)=0.000 E(IMPR)=201001.559 E(VDW )=78200.397 | ------------------------------------------------------------------------------- --------------- cycle= 20 ------ stepsize= 0.0000 ----------------------- | Etotal =386752.212 grad(E)=155.066 E(BOND)=81360.780 E(ANGL)=48233.634 | | E(DIHE)=0.000 E(IMPR)=173605.046 E(VDW )=83552.752 | ------------------------------------------------------------------------------- NBONDS: found 9650 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0000 ----------------------- | Etotal =377459.224 grad(E)=184.323 E(BOND)=86955.544 E(ANGL)=52026.859 | | E(DIHE)=0.000 E(IMPR)=154399.188 E(VDW )=84077.633 | ------------------------------------------------------------------------------- NBONDS: found 9545 intra-atom interactions NBONDS: found 9443 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =359974.837 grad(E)=264.349 E(BOND)=95630.662 E(ANGL)=57598.304 | | E(DIHE)=0.000 E(IMPR)=122308.294 E(VDW )=84437.578 | ------------------------------------------------------------------------------- NBONDS: found 9369 intra-atom interactions NBONDS: found 9357 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =330077.955 grad(E)=299.101 E(BOND)=92403.444 E(ANGL)=55795.537 | | E(DIHE)=0.000 E(IMPR)=98932.388 E(VDW )=82946.586 | ------------------------------------------------------------------------------- NBONDS: found 9355 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =297552.379 grad(E)=248.074 E(BOND)=87320.064 E(ANGL)=45239.852 | | E(DIHE)=0.000 E(IMPR)=83375.321 E(VDW )=81617.142 | ------------------------------------------------------------------------------- NBONDS: found 9379 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =278940.391 grad(E)=239.938 E(BOND)=85921.074 E(ANGL)=38512.657 | | E(DIHE)=0.000 E(IMPR)=73962.579 E(VDW )=80544.081 | ------------------------------------------------------------------------------- NBONDS: found 9433 intra-atom interactions NBONDS: found 9419 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =263386.877 grad(E)=189.934 E(BOND)=85365.442 E(ANGL)=32951.230 | | E(DIHE)=0.000 E(IMPR)=66699.159 E(VDW )=78371.046 | ------------------------------------------------------------------------------- NBONDS: found 9366 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =253405.155 grad(E)=128.388 E(BOND)=83504.229 E(ANGL)=31295.184 | | E(DIHE)=0.000 E(IMPR)=61022.715 E(VDW )=77583.027 | ------------------------------------------------------------------------------- NBONDS: found 9372 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =245648.771 grad(E)=154.032 E(BOND)=84571.147 E(ANGL)=29762.237 | | E(DIHE)=0.000 E(IMPR)=53087.197 E(VDW )=78228.190 | ------------------------------------------------------------------------------- NBONDS: found 9377 intra-atom interactions NBONDS: found 9337 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =233861.551 grad(E)=164.231 E(BOND)=85020.148 E(ANGL)=25577.106 | | E(DIHE)=0.000 E(IMPR)=45818.168 E(VDW )=77446.129 | ------------------------------------------------------------------------------- NBONDS: found 9296 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =225661.556 grad(E)=131.767 E(BOND)=84860.934 E(ANGL)=23371.413 | | E(DIHE)=0.000 E(IMPR)=41187.569 E(VDW )=76241.639 | ------------------------------------------------------------------------------- NBONDS: found 9309 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =216690.037 grad(E)=181.436 E(BOND)=85299.369 E(ANGL)=21196.965 | | E(DIHE)=0.000 E(IMPR)=35122.848 E(VDW )=75070.854 | ------------------------------------------------------------------------------- NBONDS: found 9326 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =209492.513 grad(E)=97.512 E(BOND)=82790.751 E(ANGL)=17658.016 | | E(DIHE)=0.000 E(IMPR)=33085.511 E(VDW )=75958.235 | ------------------------------------------------------------------------------- NBONDS: found 9334 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =206963.086 grad(E)=60.620 E(BOND)=82209.570 E(ANGL)=16903.198 | | E(DIHE)=0.000 E(IMPR)=32559.318 E(VDW )=75290.999 | ------------------------------------------------------------------------------- NBONDS: found 9329 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =205724.493 grad(E)=50.343 E(BOND)=82365.055 E(ANGL)=16922.265 | | E(DIHE)=0.000 E(IMPR)=31590.741 E(VDW )=74846.432 | ------------------------------------------------------------------------------- NBONDS: found 9289 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =203782.371 grad(E)=91.321 E(BOND)=83401.625 E(ANGL)=17720.680 | | E(DIHE)=0.000 E(IMPR)=27954.284 E(VDW )=74705.782 | ------------------------------------------------------------------------------- NBONDS: found 9284 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0000 ----------------------- | Etotal =198914.624 grad(E)=107.452 E(BOND)=83445.788 E(ANGL)=16072.980 | | E(DIHE)=0.000 E(IMPR)=24653.750 E(VDW )=74742.106 | ------------------------------------------------------------------------------- NBONDS: found 9264 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0000 ----------------------- | Etotal =195634.206 grad(E)=75.334 E(BOND)=82306.631 E(ANGL)=14718.601 | | E(DIHE)=0.000 E(IMPR)=23349.610 E(VDW )=75259.364 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =194352.345 grad(E)=49.205 E(BOND)=82460.967 E(ANGL)=14709.330 | | E(DIHE)=0.000 E(IMPR)=22532.954 E(VDW )=74649.094 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=200 DYNAmics> timestep=0.001 ! default DYNAmics> iasvel=maxwell DYNAmics> firsttemp=300 DYNAmics> tcoupling=true DYNAmics> tbath=300 DYNAmics> nprint=50 DYNAmics> iprfrq=0 DYNAmics>end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 755572433. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 33.90000 0.51919 0.49631 velocity [A/ps] : -0.02814 0.06034 0.03358 ang. mom. [amu A/ps] : -1073.76042 188653.91355 102367.91127 kin. ener. [Kcal/mol] : 0.44984 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 33.90000 0.51919 0.49631 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=194951.087 E(kin)=598.741 temperature=296.701 | | Etotal =194352.345 grad(E)=49.205 E(BOND)=82460.967 E(ANGL)=14709.330 | | E(DIHE)=0.000 E(IMPR)=22532.954 E(VDW )=74649.094 | ------------------------------------------------------------------------------- NBONDS: found 9211 intra-atom interactions --------------- step= 50 at 0.05000 ps -------------------------------- | E(kin)+E(total)=193060.051 E(kin)=1750.590 temperature=867.491 | | Etotal =191309.461 grad(E)=86.127 E(BOND)=82946.955 E(ANGL)=13691.911 | | E(DIHE)=0.000 E(IMPR)=21195.625 E(VDW )=73474.969 | ------------------------------------------------------------------------------- NBONDS: found 9212 intra-atom interactions NBONDS: found 9216 intra-atom interactions --------------- step= 100 at 0.10000 ps -------------------------------- | E(kin)+E(total)=189784.410 E(kin)=964.547 temperature=477.974 | | Etotal =188819.863 grad(E)=49.191 E(BOND)=82056.731 E(ANGL)=13445.586 | | E(DIHE)=0.000 E(IMPR)=19723.874 E(VDW )=73593.672 | ------------------------------------------------------------------------------- NBONDS: found 9225 intra-atom interactions NBONDS: found 9215 intra-atom interactions --------------- step= 150 at 0.15000 ps -------------------------------- | E(kin)+E(total)=186430.751 E(kin)=1246.585 temperature=617.735 | | Etotal =185184.166 grad(E)=56.444 E(BOND)=81971.348 E(ANGL)=12408.882 | | E(DIHE)=0.000 E(IMPR)=17099.030 E(VDW )=73704.907 | ------------------------------------------------------------------------------- NBONDS: found 9203 intra-atom interactions NBONDS: found 9198 intra-atom interactions --------------- step= 200 at 0.20000 ps -------------------------------- | E(kin)+E(total)=183038.587 E(kin)=1095.666 temperature=542.948 | | Etotal =181942.921 grad(E)=46.735 E(BOND)=81813.337 E(ANGL)=11681.458 | | E(DIHE)=0.000 E(IMPR)=15099.984 E(VDW )=73348.142 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 33.90000 0.51919 0.49631 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> rconst=2 NBDSET> nbxmod=-3 NBDSET> repel=0.75 ! Repulsive non-bonded energy only NBDSET> end PARRDR>end X-PLOR> X-PLOR>minimize powell nstep=400 nprint=25 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 7886 intra-atom interactions NBONDS: found 8453 intra-atom interactions NBONDS: found 9071 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =23629.532 grad(E)=273.253 E(BOND)=4600.715 E(ANGL)=11773.792 | | E(DIHE)=0.000 E(IMPR)=7175.046 E(VDW )=79.979 | ------------------------------------------------------------------------------- NBONDS: found 9508 intra-atom interactions NBONDS: found 9708 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =8976.185 grad(E)=96.585 E(BOND)=1057.065 E(ANGL)=5370.185 | | E(DIHE)=0.000 E(IMPR)=2434.417 E(VDW )=114.518 | ------------------------------------------------------------------------------- NBONDS: found 9783 intra-atom interactions NBONDS: found 9872 intra-atom interactions --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =3219.884 grad(E)=84.423 E(BOND)=421.867 E(ANGL)=2341.462 | | E(DIHE)=0.000 E(IMPR)=319.113 E(VDW )=137.442 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =1607.413 grad(E)=25.938 E(BOND)=160.029 E(ANGL)=1151.914 | | E(DIHE)=0.000 E(IMPR)=169.220 E(VDW )=126.250 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =1088.370 grad(E)=28.136 E(BOND)=94.208 E(ANGL)=718.338 | | E(DIHE)=0.000 E(IMPR)=105.987 E(VDW )=169.837 | ------------------------------------------------------------------------------- NBONDS: found 10168 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =826.809 grad(E)=16.274 E(BOND)=59.677 E(ANGL)=504.486 | | E(DIHE)=0.000 E(IMPR)=70.395 E(VDW )=192.250 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =644.480 grad(E)=12.689 E(BOND)=43.104 E(ANGL)=360.481 | | E(DIHE)=0.000 E(IMPR)=56.017 E(VDW )=184.877 | ------------------------------------------------------------------------------- NBONDS: found 10361 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =544.261 grad(E)=11.773 E(BOND)=36.125 E(ANGL)=302.942 | | E(DIHE)=0.000 E(IMPR)=46.619 E(VDW )=158.575 | ------------------------------------------------------------------------------- --------------- cycle= 225 ------ stepsize= 0.0001 ----------------------- | Etotal =455.148 grad(E)=15.901 E(BOND)=30.718 E(ANGL)=256.308 | | E(DIHE)=0.000 E(IMPR)=38.374 E(VDW )=129.748 | ------------------------------------------------------------------------------- --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =371.382 grad(E)=9.631 E(BOND)=28.643 E(ANGL)=219.578 | | E(DIHE)=0.000 E(IMPR)=23.263 E(VDW )=99.898 | ------------------------------------------------------------------------------- --------------- cycle= 275 ------ stepsize= 0.0001 ----------------------- | Etotal =316.021 grad(E)=6.443 E(BOND)=21.519 E(ANGL)=190.567 | | E(DIHE)=0.000 E(IMPR)=18.201 E(VDW )=85.735 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =287.212 grad(E)=4.953 E(BOND)=19.268 E(ANGL)=172.416 | | E(DIHE)=0.000 E(IMPR)=16.278 E(VDW )=79.250 | ------------------------------------------------------------------------------- NBONDS: found 10439 intra-atom interactions --------------- cycle= 325 ------ stepsize= 0.0001 ----------------------- | Etotal =266.805 grad(E)=2.950 E(BOND)=18.943 E(ANGL)=161.518 | | E(DIHE)=0.000 E(IMPR)=15.037 E(VDW )=71.306 | ------------------------------------------------------------------------------- --------------- cycle= 350 ------ stepsize= 0.0000 ----------------------- | Etotal =254.032 grad(E)=3.239 E(BOND)=20.114 E(ANGL)=156.423 | | E(DIHE)=0.000 E(IMPR)=14.046 E(VDW )=63.448 | ------------------------------------------------------------------------------- --------------- cycle= 375 ------ stepsize= 0.0001 ----------------------- | Etotal =243.093 grad(E)=3.618 E(BOND)=17.635 E(ANGL)=153.185 | | E(DIHE)=0.000 E(IMPR)=14.170 E(VDW )=58.103 | ------------------------------------------------------------------------------- --------------- cycle= 400 ------ stepsize= 0.0000 ----------------------- | Etotal =234.077 grad(E)=3.351 E(BOND)=16.606 E(ANGL)=148.341 | | E(DIHE)=0.000 E(IMPR)=14.204 E(VDW )=54.926 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=1000 DYNAmics> timestep=0.005 DYNAmics> iasvel=maxwell DYNAmics> firsttemp=300 DYNAmics> tcoupling=true DYNAmics> tbath=300 DYNAmics> nprint=100 DYNAmics> iprfrq=0 DYNAmics>end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 126172278. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 33.90000 0.51919 0.49631 velocity [A/ps] : -0.07129 -0.17045 -0.03831 ang. mom. [amu A/ps] : -9987.79876 199955.22987 -63329.42002 kin. ener. [Kcal/mol] : 2.88027 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 33.90000 0.51919 0.49631 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=851.639 E(kin)=617.562 temperature=306.028 | | Etotal =234.077 grad(E)=3.351 E(BOND)=16.606 E(ANGL)=148.341 | | E(DIHE)=0.000 E(IMPR)=14.204 E(VDW )=54.926 | ------------------------------------------------------------------------------- --------------- step= 100 at 0.50000 ps -------------------------------- | E(kin)+E(total)=14935.973 E(kin)=2469.374 temperature=1223.679 | | Etotal =12466.599 grad(E)=573.815 E(BOND)=1370.537 E(ANGL)=1955.602 | | E(DIHE)=0.000 E(IMPR)=9091.908 E(VDW )=48.553 | ------------------------------------------------------------------------------- --------------- step= 200 at 1.00000 ps -------------------------------- | E(kin)+E(total)=16247.942 E(kin)=1995.435 temperature=988.822 | | Etotal =14252.507 grad(E)=643.029 E(BOND)=990.138 E(ANGL)=1698.379 | | E(DIHE)=0.000 E(IMPR)=11516.730 E(VDW )=47.261 | ------------------------------------------------------------------------------- --------------- step= 300 at 1.50000 ps -------------------------------- | E(kin)+E(total)=15974.256 E(kin)=2466.840 temperature=1222.423 | | Etotal =13507.416 grad(E)=603.456 E(BOND)=1256.999 E(ANGL)=1823.554 | | E(DIHE)=0.000 E(IMPR)=10379.874 E(VDW )=46.988 | ------------------------------------------------------------------------------- --------------- step= 400 at 2.00000 ps -------------------------------- | E(kin)+E(total)=14695.863 E(kin)=2125.075 temperature=1053.064 | | Etotal =12570.789 grad(E)=586.117 E(BOND)=992.905 E(ANGL)=1823.707 | | E(DIHE)=0.000 E(IMPR)=9709.824 E(VDW )=44.353 | ------------------------------------------------------------------------------- NBONDS: found 10447 intra-atom interactions --------------- step= 500 at 2.50000 ps -------------------------------- | E(kin)+E(total)=15835.156 E(kin)=2712.122 temperature=1343.971 | | Etotal =13123.033 grad(E)=603.531 E(BOND)=1260.437 E(ANGL)=1846.455 | | E(DIHE)=0.000 E(IMPR)=9974.373 E(VDW )=41.768 | ------------------------------------------------------------------------------- --------------- step= 600 at 3.00000 ps -------------------------------- | E(kin)+E(total)=14075.701 E(kin)=2236.764 temperature=1108.411 | | Etotal =11838.936 grad(E)=533.252 E(BOND)=1757.673 E(ANGL)=2033.053 | | E(DIHE)=0.000 E(IMPR)=8007.853 E(VDW )=40.358 | ------------------------------------------------------------------------------- --------------- step= 700 at 3.50000 ps -------------------------------- | E(kin)+E(total)=16109.915 E(kin)=2185.094 temperature=1082.806 | | Etotal =13924.821 grad(E)=622.720 E(BOND)=1124.731 E(ANGL)=1630.820 | | E(DIHE)=0.000 E(IMPR)=11131.871 E(VDW )=37.399 | ------------------------------------------------------------------------------- --------------- step= 800 at 4.00000 ps -------------------------------- | E(kin)+E(total)=13161.824 E(kin)=2170.639 temperature=1075.643 | | Etotal =10991.185 grad(E)=534.230 E(BOND)=1085.729 E(ANGL)=1873.077 | | E(DIHE)=0.000 E(IMPR)=7993.966 E(VDW )=38.413 | ------------------------------------------------------------------------------- --------------- step= 900 at 4.50000 ps -------------------------------- | E(kin)+E(total)=12472.660 E(kin)=2184.041 temperature=1082.284 | | Etotal =10288.619 grad(E)=508.957 E(BOND)=1209.904 E(ANGL)=1961.491 | | E(DIHE)=0.000 E(IMPR)=7080.973 E(VDW )=36.251 | ------------------------------------------------------------------------------- --------------- step= 1000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=15420.434 E(kin)=2089.886 temperature=1035.626 | | Etotal =13330.547 grad(E)=613.156 E(BOND)=1041.577 E(ANGL)=1643.633 | | E(DIHE)=0.000 E(IMPR)=10613.222 E(VDW )=32.116 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 33.90000 0.51919 0.49631 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR>! H-building won't actually place protons, since we're using a fully protonated X-PLOR>! topology/parameter set, but it may improve their positions X-PLOR>! We're using "nbonds repel", so the "elec" flag is irrelevant X-PLOR> X-PLOR>flags exclude vdw end X-PLOR>vector do (mass=1) (name h*) SELRPN: 230 atoms have been selected out of 677 X-PLOR>hbuild selection=(name h*) phistep=360 end SELRPN: 230 atoms have been selected out of 677 HBUILD: dihedral PHI STePs for spin = 360.0000 HBUILD: cutoff during water acceptor search = 7.5000 HBUILD: H5' ,H5'', placed for donor A 1 GUA C5' . HBUILD: H4' , , placed for donor A 1 GUA C4' . HBUILD: H1' , , placed for donor A 1 GUA C1' . HBUILD: H1 , , placed for donor A 1 GUA N1 . HBUILD: H8 , , placed for donor A 1 GUA C8 . HBUILD: H2' , , placed for donor A 1 GUA C2' . HBUILD: H3' , , placed for donor A 1 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 2 GUA C5' . HBUILD: H4' , , placed for donor A 2 GUA C4' . HBUILD: H1' , , placed for donor A 2 GUA C1' . HBUILD: H1 , , placed for donor A 2 GUA N1 . HBUILD: H8 , , placed for donor A 2 GUA C8 . HBUILD: H2' , , placed for donor A 2 GUA C2' . HBUILD: H3' , , placed for donor A 2 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 3 CYT C5' . HBUILD: H4' , , placed for donor A 3 CYT C4' . HBUILD: H1' , , placed for donor A 3 CYT C1' . HBUILD: H6 , , placed for donor A 3 CYT C6 . HBUILD: H5 , , placed for donor A 3 CYT C5 . HBUILD: H2' , , placed for donor A 3 CYT C2' . HBUILD: H3' , , placed for donor A 3 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 4 ADE C5' . HBUILD: H4' , , placed for donor A 4 ADE C4' . HBUILD: H1' , , placed for donor A 4 ADE C1' . HBUILD: H2 , , placed for donor A 4 ADE C2 . HBUILD: H8 , , placed for donor A 4 ADE C8 . HBUILD: H2' , , placed for donor A 4 ADE C2' . HBUILD: H3' , , placed for donor A 4 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 5 GUA C5' . HBUILD: H4' , , placed for donor A 5 GUA C4' . HBUILD: H1' , , placed for donor A 5 GUA C1' . HBUILD: H1 , , placed for donor A 5 GUA N1 . HBUILD: H8 , , placed for donor A 5 GUA C8 . HBUILD: H2' , , placed for donor A 5 GUA C2' . HBUILD: H3' , , placed for donor A 5 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 6 GUA C5' . HBUILD: H4' , , placed for donor A 6 GUA C4' . HBUILD: H1' , , placed for donor A 6 GUA C1' . HBUILD: H1 , , placed for donor A 6 GUA N1 . HBUILD: H8 , , placed for donor A 6 GUA C8 . HBUILD: H2' , , placed for donor A 6 GUA C2' . HBUILD: H3' , , placed for donor A 6 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 7 GUA C5' . HBUILD: H4' , , placed for donor A 7 GUA C4' . HBUILD: H1' , , placed for donor A 7 GUA C1' . HBUILD: H1 , , placed for donor A 7 GUA N1 . HBUILD: H8 , , placed for donor A 7 GUA C8 . HBUILD: H2' , , placed for donor A 7 GUA C2' . HBUILD: H3' , , placed for donor A 7 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 8 CYT C5' . HBUILD: H4' , , placed for donor A 8 CYT C4' . HBUILD: H1' , , placed for donor A 8 CYT C1' . HBUILD: H6 , , placed for donor A 8 CYT C6 . HBUILD: H5 , , placed for donor A 8 CYT C5 . HBUILD: H2' , , placed for donor A 8 CYT C2' . HBUILD: H3' , , placed for donor A 8 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 9 URI C5' . HBUILD: H4' , , placed for donor A 9 URI C4' . HBUILD: H1' , , placed for donor A 9 URI C1' . HBUILD: H6 , , placed for donor A 9 URI C6 . HBUILD: H3 , , placed for donor A 9 URI N3 . HBUILD: H5 , , placed for donor A 9 URI C5 . HBUILD: H2' , , placed for donor A 9 URI C2' . HBUILD: H3' , , placed for donor A 9 URI C3' . HBUILD: H5' ,H5'', placed for donor A 10 CYT C5' . HBUILD: H4' , , placed for donor A 10 CYT C4' . HBUILD: H1' , , placed for donor A 10 CYT C1' . HBUILD: H6 , , placed for donor A 10 CYT C6 . HBUILD: H5 , , placed for donor A 10 CYT C5 . HBUILD: H2' , , placed for donor A 10 CYT C2' . HBUILD: H3' , , placed for donor A 10 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 11 ADE C5' . HBUILD: H4' , , placed for donor A 11 ADE C4' . HBUILD: H1' , , placed for donor A 11 ADE C1' . HBUILD: H2 , , placed for donor A 11 ADE C2 . HBUILD: H8 , , placed for donor A 11 ADE C8 . HBUILD: H2' , , placed for donor A 11 ADE C2' . HBUILD: H3' , , placed for donor A 11 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 12 URI C5' . HBUILD: H4' , , placed for donor A 12 URI C4' . HBUILD: H1' , , placed for donor A 12 URI C1' . HBUILD: H6 , , placed for donor A 12 URI C6 . HBUILD: H3 , , placed for donor A 12 URI N3 . HBUILD: H5 , , placed for donor A 12 URI C5 . HBUILD: H2' , , placed for donor A 12 URI C2' . HBUILD: H3' , , placed for donor A 12 URI C3' . HBUILD: H5' ,H5'', placed for donor A 13 ADE C5' . HBUILD: H4' , , placed for donor A 13 ADE C4' . HBUILD: H1' , , placed for donor A 13 ADE C1' . HBUILD: H2 , , placed for donor A 13 ADE C2 . HBUILD: H8 , , placed for donor A 13 ADE C8 . HBUILD: H2' , , placed for donor A 13 ADE C2' . HBUILD: H3' , , placed for donor A 13 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 14 ADE C5' . HBUILD: H4' , , placed for donor A 14 ADE C4' . HBUILD: H1' , , placed for donor A 14 ADE C1' . HBUILD: H2 , , placed for donor A 14 ADE C2 . HBUILD: H8 , , placed for donor A 14 ADE C8 . HBUILD: H2' , , placed for donor A 14 ADE C2' . HBUILD: H3' , , placed for donor A 14 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 15 CYT C5' . HBUILD: H4' , , placed for donor A 15 CYT C4' . HBUILD: H1' , , placed for donor A 15 CYT C1' . HBUILD: H6 , , placed for donor A 15 CYT C6 . HBUILD: H5 , , placed for donor A 15 CYT C5 . HBUILD: H2' , , placed for donor A 15 CYT C2' . HBUILD: H3' , , placed for donor A 15 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 16 CYT C5' . HBUILD: H4' , , placed for donor A 16 CYT C4' . HBUILD: H1' , , placed for donor A 16 CYT C1' . HBUILD: H6 , , placed for donor A 16 CYT C6 . HBUILD: H5 , , placed for donor A 16 CYT C5 . HBUILD: H2' , , placed for donor A 16 CYT C2' . HBUILD: H3' , , placed for donor A 16 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 17 CYT C5' . HBUILD: H4' , , placed for donor A 17 CYT C4' . HBUILD: H1' , , placed for donor A 17 CYT C1' . HBUILD: H6 , , placed for donor A 17 CYT C6 . HBUILD: H5 , , placed for donor A 17 CYT C5 . HBUILD: H2' , , placed for donor A 17 CYT C2' . HBUILD: H3' , , placed for donor A 17 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 18 URI C5' . HBUILD: H4' , , placed for donor A 18 URI C4' . HBUILD: H1' , , placed for donor A 18 URI C1' . HBUILD: H6 , , placed for donor A 18 URI C6 . HBUILD: H3 , , placed for donor A 18 URI N3 . HBUILD: H5 , , placed for donor A 18 URI C5 . HBUILD: H2' , , placed for donor A 18 URI C2' . HBUILD: H3' , , placed for donor A 18 URI C3' . HBUILD: H5' ,H5'', placed for donor A 19 GUA C5' . HBUILD: H4' , , placed for donor A 19 GUA C4' . HBUILD: H1' , , placed for donor A 19 GUA C1' . HBUILD: H1 , , placed for donor A 19 GUA N1 . HBUILD: H8 , , placed for donor A 19 GUA C8 . HBUILD: H2' , , placed for donor A 19 GUA C2' . HBUILD: H3' , , placed for donor A 19 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 20 CYT C5' . HBUILD: H4' , , placed for donor A 20 CYT C4' . HBUILD: H1' , , placed for donor A 20 CYT C1' . HBUILD: H6 , , placed for donor A 20 CYT C6 . HBUILD: H5 , , placed for donor A 20 CYT C5 . HBUILD: H2' , , placed for donor A 20 CYT C2' . HBUILD: H3' , , placed for donor A 20 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 21 CYT C5' . HBUILD: H4' , , placed for donor A 21 CYT C4' . HBUILD: H1' , , placed for donor A 21 CYT C1' . HBUILD: H6 , , placed for donor A 21 CYT C6 . HBUILD: H5 , , placed for donor A 21 CYT C5 . HBUILD: H2' , , placed for donor A 21 CYT C2' . HBUILD: H3' , , placed for donor A 21 CYT C3' . HBUILD: H5T , , , constructed (spin) for donor A 1 GUA O5T . HBUILD: H21 ,H22 , , constructed (spin) for donor A 1 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 1 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 2 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 2 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 3 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 3 CYT O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 4 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 4 ADE O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 5 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 5 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 6 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 6 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 7 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 7 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 8 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 8 CYT O2' . HBUILD: HO2', , , constructed (spin) for donor A 9 URI O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 10 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 10 CYT O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 11 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 11 ADE O2' . HBUILD: HO2', , , constructed (spin) for donor A 12 URI O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 13 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 13 ADE O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 14 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 14 ADE O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 15 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 15 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 16 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 16 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 17 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 17 CYT O2' . HBUILD: HO2', , , constructed (spin) for donor A 18 URI O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 19 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 19 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 20 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 20 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 21 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 21 CYT O2' . HBUILD: H3T , , , constructed (spin) for donor A 21 CYT O3' . X-PLOR> X-PLOR>flags include vdw end X-PLOR>minimize powell nstep=800 nprint=50 end POWELL: number of degrees of freedom= 2031 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 10397 intra-atom interactions NBONDS: found 10400 intra-atom interactions NBONDS: found 10440 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =511.315 grad(E)=27.708 E(BOND)=49.757 E(ANGL)=135.990 | | E(DIHE)=0.000 E(IMPR)=277.026 E(VDW )=48.542 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =168.335 grad(E)=4.287 E(BOND)=10.886 E(ANGL)=95.904 | | E(DIHE)=0.000 E(IMPR)=17.166 E(VDW )=44.379 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =151.373 grad(E)=2.096 E(BOND)=9.266 E(ANGL)=90.927 | | E(DIHE)=0.000 E(IMPR)=11.281 E(VDW )=39.900 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =142.445 grad(E)=2.263 E(BOND)=8.844 E(ANGL)=87.325 | | E(DIHE)=0.000 E(IMPR)=11.174 E(VDW )=35.102 | ------------------------------------------------------------------------------- --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =134.996 grad(E)=2.148 E(BOND)=8.056 E(ANGL)=83.326 | | E(DIHE)=0.000 E(IMPR)=11.407 E(VDW )=32.207 | ------------------------------------------------------------------------------- NBONDS: found 10435 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =124.659 grad(E)=2.520 E(BOND)=7.214 E(ANGL)=77.629 | | E(DIHE)=0.000 E(IMPR)=12.383 E(VDW )=27.433 | ------------------------------------------------------------------------------- --------------- cycle= 350 ------ stepsize= 0.0000 ----------------------- | Etotal =116.327 grad(E)=1.748 E(BOND)=6.408 E(ANGL)=75.634 | | E(DIHE)=0.000 E(IMPR)=10.894 E(VDW )=23.391 | ------------------------------------------------------------------------------- --------------- cycle= 400 ------ stepsize= 0.0000 ----------------------- | Etotal =111.535 grad(E)=1.611 E(BOND)=6.169 E(ANGL)=73.956 | | E(DIHE)=0.000 E(IMPR)=10.370 E(VDW )=21.042 | ------------------------------------------------------------------------------- --------------- cycle= 450 ------ stepsize= 0.0000 ----------------------- | Etotal =107.321 grad(E)=1.441 E(BOND)=5.509 E(ANGL)=71.713 | | E(DIHE)=0.000 E(IMPR)=10.002 E(VDW )=20.097 | ------------------------------------------------------------------------------- --------------- cycle= 500 ------ stepsize= 0.0000 ----------------------- | Etotal =103.986 grad(E)=1.413 E(BOND)=5.300 E(ANGL)=70.075 | | E(DIHE)=0.000 E(IMPR)=9.582 E(VDW )=19.029 | ------------------------------------------------------------------------------- --------------- cycle= 550 ------ stepsize= 0.0000 ----------------------- | Etotal =100.321 grad(E)=1.439 E(BOND)=4.542 E(ANGL)=68.534 | | E(DIHE)=0.000 E(IMPR)=9.248 E(VDW )=17.998 | ------------------------------------------------------------------------------- --------------- cycle= 600 ------ stepsize= 0.0000 ----------------------- | Etotal =96.409 grad(E)=1.437 E(BOND)=3.993 E(ANGL)=66.435 | | E(DIHE)=0.000 E(IMPR)=9.098 E(VDW )=16.884 | ------------------------------------------------------------------------------- --------------- cycle= 650 ------ stepsize= 0.0000 ----------------------- | Etotal =93.085 grad(E)=1.190 E(BOND)=3.497 E(ANGL)=64.149 | | E(DIHE)=0.000 E(IMPR)=9.176 E(VDW )=16.263 | ------------------------------------------------------------------------------- NBONDS: found 10382 intra-atom interactions --------------- cycle= 700 ------ stepsize= 0.0000 ----------------------- | Etotal =90.076 grad(E)=1.280 E(BOND)=3.218 E(ANGL)=62.240 | | E(DIHE)=0.000 E(IMPR)=9.481 E(VDW )=15.138 | ------------------------------------------------------------------------------- --------------- cycle= 750 ------ stepsize= 0.0000 ----------------------- | Etotal =87.071 grad(E)=1.214 E(BOND)=3.182 E(ANGL)=60.593 | | E(DIHE)=0.000 E(IMPR)=9.007 E(VDW )=14.289 | ------------------------------------------------------------------------------- --------------- cycle= 800 ------ stepsize= 0.0000 ----------------------- | Etotal =85.344 grad(E)=0.758 E(BOND)=2.865 E(ANGL)=59.259 | | E(DIHE)=0.000 E(IMPR)=8.980 E(VDW )=14.241 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Analyze and write out the final structure. X-PLOR>! Total energy should be no more than about 100. If it is, it is probably X-PLOR>! because one or more purines are trapped in a crumpled conformation. X-PLOR> X-PLOR>flags exclude * include bond angle dihe impr vdw end X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.050: 0 RMS deviation= 0.001 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.130098E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.559 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.558910 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 0.000000E+00 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.259 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.259387 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 2.86534, angle 59.2586, dihedral 0, improper 8.97991, VdW 14.2406, total 85.3444 RMSD: bond 1.300982E-03, angle 0.55891, dihedral 0, improper 0.259387 Violations: bond 0, angle 0, dihedral 0, improper 0 X-PLOR> X-PLOR>write coordinates output=template.pdb end ASSFIL: file /sgi/people/dcs/ws/xplor/italy2.4x/template.pdb opened. X-PLOR> X-PLOR>stop CSTACK: size= 200000 used= 227 current= 0 HEAP: maximum use= 98626 current use= 0 X-PLOR: total CPU time= 43.8136 s X-PLOR: entry time at 13:40:38 27-Apr-96 X-PLOR: exit time at 13:41:22 27-Apr-96